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FF:11521-119H9: Difference between revisions

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|creation_date=
|creation_date=
|def=
|def=
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|fonse_cell_line=
|fonse_cell_line=
|fonse_cell_line_closure=
|fonse_cell_line_closure=

Revision as of 17:10, 29 March 2012


Name:Hepatic Sinusoidal Endothelial Cells, donor1
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueliver
dev stageNA
sexNA
ageNA
cell typehepatic sinusoidal endothelial cell
cell lineNA
companySciencell/3H
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberlot:1253
catalog numberSC5005
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-TRIzol-isopropanol-v1.0
Download raw sequence, BAM & CTSS
Hg19
BAMCTSS
[{{{hg19bam}}} download][{{{hg19ctss}}} donwload]
Hg38
BAMCTSS
[{{{hg38bam}}} download][{{{hg38ctss}}} donwload]


Relative expression to median (log10)

Transcription factors with enriched expression in this sampleRanked list of transcription factor promoter expression in this sample relative to the median expression in the FANTOM5 collection is shown. Value is log10 transformed.



Co-expression clusters with enriched expression in this sampleRanked list of co-expression cluster expression in this sample relative to the median expression in the FANTOM5 collection is shown. Value is log10 transformed. <br>Analyst:NA <br><br>link to dataset.<br>data

Coexpression clusterscore
C0-CD14-Eosinophils-Neutrophils-Basophils-CD34-immature-Peripheral0
C1-testis-epididymis-embryonic-medulla-pituitary-trachea-caudate0
C10-occipital-temporal-parietal-brain-duodenum-Neurons-Neural0
C100-rhabdomyosarcoma-gastric-pineal-Wilms-cervical-mesodermal-endometrial0
C101-small-cerebellum-maxillary-colon-parietal-epididymis-merkel0
C102-neuroblastoma-testicular-pituitary-carcinosarcoma-rectum-acantholytic-iPS0
C103-CD4-CD8-Natural-Peripheral-Whole-Neutrophils-Basophils0
C104-Mast-Basophils-immature-CD14-CD34-eye-Natural0
C105-heart-skeletal-occipital-hippocampus-acute-Sebocyte-penis-0.113
C106-Hep2-epitheloid-placenta-cervical-rectal-anaplastic-glassy0
C107-Neutrophils-CD14-Eosinophils-Monocytederived-Whole-Peripheral-blood0
C108-breast-hepatoblastoma-MCF7-parotid-salivary-submaxillary-prostate0
C109-Reticulocytes-non-acute-Hodgkin-Burkitt-retinoblastoma-lymphoma-0.0771
C11-cerebellum-medulla-pons-parietal-occipital-middle-medial0
C110-leukemia-chronic-Eosinophils-acute-Whole-CD34-Lymphatic0
C111-medulla-lung-trachea-testis-caudate-epididymis-throat0
C112-gastric-pancreas-temporal-duodenum-small-extraskeletal-adrenal0
C113-thyroid-throat-lung-lymph-small-colon-trachea0
C114-teratocarcinoma-medulloblastoma-carcinosarcoma-iPS-anaplastic-acute-neuroblastoma0
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C98-CD8-Natural-Basophils-blood-CD4-Peripheral-Whole0
C99-hairy-mycosis-submaxillary-salivary-cord-kidney-parotid0



Repeat families with enriched expression in this sample<b>Summary:</b>Ranked list of repeat family expression in this sample relative tothe median expression in the FANTOM5 collection is shown. Value is log10transformed.<br><b>Analyst:</b>NA<br><br>link to dataset.<br>data no result for this sample


TFBS(DNA)motifs over-represented in proximal region of promoters active in this sample

JASPAR motifs<b>Summary:</b>Association of JASPAR motif to the promoter expression in thissample. Pearson's correlation between the number of TFBSs estimated byusing the position-weight matrix for each promoter and its expression isexpressed as Z-score by taking the ones based on random position-weightmatrix, and the tail probability of the normal distribution correspondingto the Z-score is taken as the resulting P-value. Lower P-value indicatesmore (non-random) association of the motif to promoter expression<br><b>Analyst:</b> Michiel de Hoon <br><br><br>link to dataset.<br>data

library id: CNhs12075

Jaspar motifP-value
MA0002.20.838
MA0003.10.275
MA0004.10.332
MA0006.10.166
MA0007.10.00183
MA0009.10.771
MA0014.10.641
MA0017.10.0459
MA0018.22.46728e-4
MA0019.10.09
MA0024.10.107
MA0025.10.151
MA0027.10.321
MA0028.18.18871e-4
MA0029.10.267
MA0030.10.69
MA0031.10.681
MA0035.25.26018e-6
MA0038.10.564
MA0039.20.701
MA0040.10.203
MA0041.10.145
MA0042.10.685
MA0043.15.46264e-5
MA0046.10.161
MA0047.20.0911
MA0048.10.73
MA0050.10.445
MA0051.10.802
MA0052.10.466
MA0055.10.334
MA0057.10.432
MA0058.10.137
MA0059.10.872
MA0060.10.211
MA0061.10.562
MA0062.21.08792e-4
MA0065.20.106
MA0066.10.0496
MA0067.10.187
MA0068.10.681
MA0069.10.0235
MA0070.10.0611
MA0071.10.023
MA0072.10.862
MA0073.10.533
MA0074.10.426
MA0076.13.70713e-6
MA0077.17.2592e-5
MA0078.10.00105
MA0079.20.227
MA0080.20.00104
MA0081.10.437
MA0083.10.277
MA0084.10.792
MA0087.10.234
MA0088.10.981
MA0090.10.458
MA0091.10.248
MA0092.10.856
MA0093.10.303
MA0099.20.372
MA0100.10.221
MA0101.10.175
MA0102.23.64906e-5
MA0103.10.771
MA0104.20.404
MA0105.10.914
MA0106.10.0079
MA0107.10.181
MA0108.20.576
MA0111.10.771
MA0112.20.348
MA0113.10.148
MA0114.10.274
MA0115.10.974
MA0116.10.718
MA0117.10.0491
MA0119.10.126
MA0122.10.197
MA0124.10.681
MA0125.10.937
MA0131.10.0814
MA0135.10.0682
MA0136.10.351
MA0137.20.102
MA0138.20.0717
MA0139.10.204
MA0140.10.0274
MA0141.11.36549e-4
MA0142.10.936
MA0143.10.962
MA0144.10.665
MA0145.10.283
MA0146.10.0966
MA0147.10.416
MA0148.10.0192
MA0149.10.0512
MA0150.10.889
MA0152.10.502
MA0153.10.525
MA0154.10.313
MA0155.10.00492
MA0156.10.955
MA0157.10.575
MA0159.10.195
MA0160.10.0102
MA0162.10.162
MA0163.10.448
MA0164.10.375
MA0258.10.262
MA0259.10.314



FANTOM5 phase1 novel unique motifs<b>Summary:</b>Association of the 169 novel and unique motifs discovered in FANTOM5 phase1 in this sample. Among the de-novo motifs discovered by DMF, HOMER,ChIPMunk, and ScanAll, only novel motifs are selected after comparison with known motif sets, and their clustering based on MACRO-APE resulted in169 novel and unique motifs. Their association to the promoter expression is evaluated in the same way to the JASPAR motif above<br><b>Analyst:</b> Michiel de Hoon <br><br><br>link to dataset.<br>data

library id: CNhs12075

Novel motifP-value
10.944
100.566
1000.926
1010.352
1020.266
1030.266
1040.974
1050.23
1060.1
1070.0134
1080.249
1090.302
110.0466
1100.0296
1110.992
1120.516
1130.528
1140.433
1150.602
1160.627
1170.817
1180.465
1190.0822
120.666
1200.0384
1210.929
1220.681
1230.397
1240.501
1250.763
1260.613
1270.506
1280.0782
1290.154
130.462
1300.669
1310.111
1320.108
1330.228
1340.72
1350.453
1360.646
1370.216
1380.796
1390.825
140.73
1400.959
1410.357
1420.621
1430.0976
1440.431
1450.117
1460.203
1470.536
1480.19
1490.0285
150.429
1500.294
1510.682
1520.0758
1530.075
1540.165
1550.743
1560.529
1570.524
1580.869
1590.8
160.485
1600.00547
1610.903
1620.182
1630.384
1640.797
1650.448
1660.0942
1670.0693
1680.268
1690.0326
170.298
180.911
190.0981
20.252
200.695
210.939
220.102
230.18
240.713
250.631
260.416
270.0477
280.506
290.767
30.687
300.357
310.489
320.291
330.253
340.0258
350.755
360.404
370.534
380.109
390.321
40.457
400.0176
410.0213
420.88
430.538
440.417
450.131
460.204
470.623
480.238
490.604
50.901
500.691
510.24
520.581
530.775
540.345
550.981
560.491
570.524
580.636
590.0323
60.382
600.336
610.879
620.668
630.516
640.193
650.0261
660.644
670.65
680.249
690.852
70.62
700.545
710.745
720.559
730.0513
740.184
750.486
760.329
770.0253
780.509
790.267
80.0195
800.409
810.768
820.146
830.661
840.138
850.111
860.936
870.347
880.745
890.267
90.164
900.157
910.271
920.249
930.597
940.717
950.177
960.319
970.329
980.525
990.0393



de novo motifs identified by HOMER in promoters active in this sample<b>Summary:</b>The result of HOMER in this sample is shown.<br><b>Analyst:</b>NA <br> library id: CNhs12075


FANTOM5 (FF) ontology

Direct parent terms


Ancestor terms (non development)<b>Summary:</b>Connected ontology terms with is_a, part_of or located_in relationship <br><b>Analyst:</b> Hideya Kawaji<br><br>link to source data<br>data

CL: Cell type
0000000 (cell), 0000000 (cell)
0000003 (native cell)
0000066 (epithelial cell)
0000115 (endothelial cell)
0000213 (lining cell)
0000215 (barrier cell)
0000222 (mesodermal cell)
0000255 (eukaryotic cell)
0000548 (animal cell)
0002078 (meso-epithelial cell)
0002262 (endothelial cell of sinusoid)
0002321 (embryonic cell)
0002371 (somatic cell)
1000398 (endothelial cell of hepatic sinusoid)

UBERON: Anatomy
0000015 (anatomical boundary)
0000025 (tube)
0000055 (vessel)
0000061 (anatomical structure)
0000062 (organ)
0000064 (organ part)
0000077 (mixed endoderm/mesoderm-derived structure)
0000119 (cell layer)
0000353 (parenchyma)
0000465 (material anatomical entity)
0000466 (immaterial anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000475 (organism subdivision)
0000477 (anatomical cluster)
0000479 (tissue)
0000480 (anatomical group)
0000481 (multi-tissue structure)
0000483 (epithelium)
0000916 (abdomen)
0000922 (embryo)
0000923 (germ layer)
0000925 (endoderm)
0000926 (mesoderm)
0000949 (endocrine system)
0001007 (digestive system)
0001009 (circulatory system)
0001041 (foregut)
0001048 (primordium)
0001062 (anatomical entity)
0001280 (liver parenchyma)
0001281 (hepatic sinusoid)
0001555 (digestive tract)
0001981 (blood vessel)
0002049 (vasculature)
0002050 (embryonic structure)
0002100 (trunk)
0002107 (liver)
0002330 (exocrine system)
0002365 (exocrine gland)
0002368 (endocrine gland)
0002405 (immune system)
0002417 (abdominal segment of trunk)
0002423 (hepatobiliary system)
0002530 (gland)
0002532 (epiblast (generic))
0003081 (lateral plate mesoderm)
0003104 (mesenchyme)
0003497 (abdomen blood vessel)
0003513 (trunk blood vessel)
0003835 (abdominal segment blood vessel)
0003894 (liver primordium)
0003909 (sinusoid)
0003914 (epithelial tube)
0004111 (anatomical conduit)
0004119 (endoderm-derived structure)
0004120 (mesoderm-derived structure)
0004161 (septum transversum)
0004185 (endodermal part of digestive tract)
0004535 (cardiovascular system)
0004537 (blood vasculature)
0004647 (liver lobule)
0004872 (splanchnic layer of lateral plate mesoderm)
0004921 (subdivision of digestive tract)
0005057 (immune organ)
0005172 (abdomen element)
0005173 (abdominal segment element)
0005177 (trunk region element)
0005256 (trunk mesenchyme)
0005423 (developing anatomical structure)
0005911 (endo-epithelium)
0006235 (foregut-midgut junction)
0006925 (digestive gland)
0006965 (vascular cord)
0007026 (primitive gut)
0007500 (epithelial tube open at both ends)
0007798 (vascular system)
0008835 (hepatic diverticulum)
0008836 (liver bud)
0009142 (entire embryonic mesenchyme)

FF: FANTOM5
NA

Ancestor terms (development)<b>Summary:</b>Connected ontology terms with develops_from, derives_from or preceded_by relationship <br><b>Analyst:</b> Hideya Kawaji <br><br>link to source data<br>data
NA

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